I believe that you are not familiar with what a shift rod adjustment is or how to check the required height. It is not related to the boat's shifting cable adjustment.
Has your gearcase been removed before for perhaps a water pump replacement or some other reason? If so, then it may have been installed without first adjusting the shift rod, as the rod is easily rotated on removal or installation.
The shift cable trunion that you describe is only for centering the shift cable "throw" to equalize the distance between forward and reverse travel.
Because you bought the boat used, it may be best to have a factory trained tech check over the linkage condition, shift rod adjustment, possible wear on reverse gear and clutch dog, and an overall evaluation of your motor, plus any updates it may need.
"There is never just one thing wrong with a boat";
-- Travis McGee, main character in a book series by John D. McDonald
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The factory recommends that a properly trained technician service your Johnson or Evinrude outboard motor. Should you elect to perform repairs yourself, use caution, common sense, and observe safety procedures in the vicinity of flammable liquids, around moving parts, near high-temperature components, and working with electrical or ignition systems.
The information offered here is only general in nature and should not be construed as complete factory approved procedures, techniques, or specifications. Always use the proper service manual for your motor, up-to-date service literature, the correct tools, and have an understanding of how to proceed with troubleshooting and repair methods. If you are unsure or uncomfortable with a procedure, a situation, or a technique, enlist the services of a factory trained technician.
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